6M0S

3.6A Yeast Vo state3 prime


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V o complex.

Roh, S.H.Shekhar, M.Pintilie, G.Chipot, C.Wilkens, S.Singharoy, A.Chiu, W.

(2020) Sci Adv 6

  • DOI: 10.1126/sciadv.abb9605
  • Primary Citation of Related Structures:  
    6M0R, 6M0S

  • PubMed Abstract: 
  • Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a V o proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive ...

    Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a V o proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo-electron microscopy (cryo-EM) structure of yeast V o proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of V o that shows the c -ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with c -ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free V o that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.


    Organizational Affiliation

    Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit a, vacuolar isoformA825Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPH1YOR270C
Membrane Entity: Yes 
UniProt
Find proteins for P32563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit eB [auth M]71Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA9CWH36LDB10YCL005W-A
Membrane Entity: Yes 
UniProt
Find proteins for Q3E7B6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein YPR170W-BC [auth O]69Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YPR170W-B
Membrane Entity: Yes 
UniProt
Find proteins for P0C5R9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit dD [auth B]345Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA6YLR447CL9324.8
Membrane Entity: Yes 
UniProt
Find proteins for P32366 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit c''E [auth C]198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA16PPA1YHR026W
Membrane Entity: Yes 
UniProt
Find proteins for P23968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit c'F [auth D]158Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA11CLS9TFP3YPL234CP1064
Membrane Entity: Yes 
UniProt
Find proteins for P32842 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
V-type proton ATPase subunit cG [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L]159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VMA3CLS7CUP5GEF2YEL027W
Membrane Entity: Yes 
UniProt
Find proteins for P25515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
V0 assembly protein 1O [auth N]52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VOA1YGR106C
Membrane Entity: Yes 
UniProt
Find proteins for P53262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM058600
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079429
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10OD021600
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2019M3E5D6063865
National Science Foundation (NSF, United States)United StatesMCB-1942763
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM067887
Agence Nationale de la Recherche (ANR)FranceProteaseInAction Grant

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release